SAN DIEGO—When Agena Bioscience Inc. acquired the bioscience business of Sequenom Inc. in a deal worth $35.8 million recently, Chairman and interim CEO John Lillig set his sights on broadening Agena’s global presence, expanding its diagnostic market and advancing its UltraSEEK technology, reportedly the first ultrasensitive somatic mutation detection technology for high-throughput of rare mutations that occur at less than 1 percent abundance in matched tissue, circulating plasma and tumor samples.

 

Lillig has already made the UltraSEEK Oncogene Panel available to researchers. This panel uses 40 nanograms of input DNA to interrogate 26 driver mutations in 12 critical oncogenes, the company says. An online tool for designing custom UltraSEEK panels for ultrasensitive interrogation of low-level mutations on the MassARRAY System will be available to the clinical research community later this year.

 

“UltraSEEK puts us on the cusp of understanding how to treat chronic diseases,” Lillig says. “For investigators interested in liquid biopsies to monitor therapeutic response, the unsurpassed sensitivity and throughput that the UltraSEEK technology affords allows acquisition of the biological data necessary to address resistance to targeted inhibitors and/or minimal residual disease.”

 

For instance, tumors harbor many cells with differing genetic mutations, he notes. While some of these cells may contain mutations that confer resistance to targeted inhibitors, they may comprise such a miniscule component of the tumor that these cells are not detected using standard genotyping and sequencing methodologies. Those methodologies have analytical sensitivity limited to mutations at 5 to 10 percent abundance.

 

Other methodologies also “restrict analysis to solid tumor samples and force compromise between sample number and depth of coverage,” Lillig explains. “In the rare case, low-level mutations were detected using newer methodologies such as digital PCR. Few if any studies have addressed the utility of these low-level mutations in the context of therapeutic response.”

 

The UltraSEEK technology enhances the sensitivity of the single-allele base extension reaction (SABER) method for MassARRAY genotyping, Agena states. The SABER method was recently employed by Dr. Kazuto Nishio and colleagues at Kinki University in Osaka, Japan, and several Japanese medical centers to profile lung cancer-related gene fusions and rare somatic hotspot mutations that may affect patients’ therapeutic responses in a Phase 3 trial of multiple lung cancer drugs. Data from the study were presented at the American Society for Clinical Oncology annual meeting in Chicago on May 31.

 

“Certain cancer therapeutics are extremely effective at shrinking specific tumor types, such as treating non-small cell lung cancer with anti-EGFR inhibitors,” Lillig says. “Dr. Nishio’s study indicates that detecting in blood plasma a low-level mutation such as T790M, which occurs at a frequency sometimes below 0.5 percent, may indicate future tumor regrowth and the need to assess an alternative treatment plan.”

 

The beauty is, the entire workflow for the UltraSEEK panels, from extracted sample DNA to the final mutation report, can be completed in a single day.

 

The company’s vision is to leverage the unique capabilities of the MassARRAY platform and make it an informative and cost-effective genetic analysis tool for use in clinical practice.

 

“Our team has been greatly impressed by the MassARRAY platform’s power to deliver accurate and cost-effective characterization of nucleic acids,” Matt Mackowski, chairman of Telegraph Hill Partners (THP), stated in a May 30 news release. “Sequenom management and THP agree that this transaction will allow the highly talented staff of the bioscience business to focus their energies on expanding the potential of the platform.”

 

“We are delighted to accelerate this transformation through the support of THP’s growth capital,” he added.

 

According to Lillig, the MassARRAY “has become a fundamental tool for genomic research. We believe it will have a similar impact as a high-throughput and cost-effective workhorse technology for mutation detection and targeted genomic analysis of cancer and other diseases in the clinical laboratory setting as well.”

 

With a renewed interest in genetics, Agena believes the demand for the MassARRAY technology will only get stronger.

 

Already utilized in more than 2,000 published research studies, the MassARRAY technology incorporates MALDI-TOF mass spectrometry for highly sensitive and specific interrogation of tens to hundreds of multiplexed genetic biomarkers at a low cost point, Agena notes. The MassARRAY instrument and accompanying custom and predesigned assay kits have been used to validate candidate markers at a high sample throughput, enabling statistically significant correlations to clinically relevant phenotypes. The results of these studies subsequently are used to develop molecular diagnostics.

 

Fritz Eibel, head of commercial operations at Agena, says the company intends to “leverage the unique capabilities of the MassARRAY system and make it an informative and cost- effective genetic analysis tool for use in clinical practice.”

 

The MassARRAY System is offered in two formats—the 96-well and the 384-well—which retail for $240,000 and $375,000 respectively, Eibel said.

 

 “Agena Bioscience intends to foster organic growth of the research market it currently serves while concurrently expanding into the clinical diagnostic segment,” Eibel says. “Specifically, Agena will follow a three-pronged approach: One, to continue to fund and develop products including panels, software and chemistries to empower clinical and translational research; two, to develop IVD content that capitalizes on the economic efficiencies and technical benefits of MALDI-TOF mass spectrometry; and three, partner with key collaborators to support the development of companion diagnostics for precision medicine.”

 

Currently, Agena Bioscience has a footprint in 38 countries worldwide, and is actively pursuing collaborations and distribution channels, he says.

 

While the MassARRAY System “has been proven in the research setting, it is just starting to be routinely utilized in a clinical setting,” Eibel says. “The platform is ideal for fulfilling many of the unmet needs in this segment. Agena will harness the power of the MassARRAY and deploy it into the clinical segment while continuing to grow and support our research and ag-bio customers.”

 

Under the terms of the agreement, Sequenom received a cash payment of $31.8 million, subject to certain adjustments, and may also receive up to $4 million in contingent consideration upon the achievement of certain regulatory and sales milestones.

 

Agena Bioscience also assumed certain liabilities related to Sequenom. The facility lease for its bioscience location in San Diego was also assumed by Agena Bioscience and all of Sequenom’s current bioscience employees will be offered employment by Agena Bioscience.

 

“We are pleased to sell the business to Agena Bioscience and Telegraph Hill Partners as they plan to invest in the growth of the bioscience business to achieve its full potential,” stated Harry F. Hixson Jr., chairman and CEO of Sequenom. “This sale strengthens our balance sheet, and will enable us to focus exclusively on our Sequenom Laboratories business as we work toward achieving profitability.”